Merge branch 'feature-s/cleanup' into 'dev'

remove unused views and routes

Closes #3076

See merge request !170

server/web2py/applications/vidjil/views/patient/confirm.html

-{{extend 'db_layout.html'}}
-{{import vidjil_utils}}
-
-{{('message' in globals())}}
-{{if 'message' in globals():}}
-
-{{
-data_count = 0 
-patient_name = vidjil_utils.anon_ids(request.vars["id"])
-sequence_count = db( (db.sequence_file.id == db.sample_set_membership.sequence_file_id)
-            &(db.sample_set_membership.sample_set_id == db.patient.sample_set_id)
-            &(db.patient.id == request.vars["id"])).count()
-data_count = db( (db.sequence_file.id == db.sample_set_membership.sequence_file_id)
-            &(db.sample_set_membership.sample_set_id == db.patient.sample_set_id)
-            &(db.patient.id == request.vars["id"])
-            &(db.results_file.sequence_file_id == db.sequence_file.id)).count()
-}}
-<div>
-    <h3>{{=message}}: {{=patient_name}}
-    </h3>
-    
-    Are you sure you want to delete the patient {{=patient_name}} ?</br>
-    This will delete {{=sequence_count}} sequence file(s) and {{=data_count}} result files.</br>
-    This action cannot be undone.
-
-    <div class="center"> 
-        <button onclick="db.call('patient/delete', {'id' :'{{=request.vars["id"]}}'} )">delete</button>
-        <button onclick="db.call('patient/index')">cancel</button>
-    </div>
-</div>
-    
-{{elif 'content' in globals():}}
-{{=content}}
-{{else:}}
-{{=BEAUTIFY(response._vars)}}
-{{pass}}

server/web2py/applications/vidjil/views/patient/index.html

-{{extend 'db_layout.html'}}
-{{import vidjil_utils}}
-
-{{total_file_count = 0 ; total_size = 0}}
-
-<h3></h3>
-
-<div class="db_block">
-    <div class="db_block_left">
-        search
-        <input id="db_filter_input" type="text" value="{{=request.vars["filter"]}}"  onchange="db.call('patient/index', {'filter' : this.value} )">
-    </div>
-</div>
-
-<div id="db_table_container">
-    <table class="db_table" id="table">
-
-
-        <thead>
-            <tr><td class="column_200 pointer" onclick="db.call('patient/index', {'sort' :'last_name', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="last_name" :}} , 'reverse' : true {{pass}} })"> name </td>
-                <td class="column_100 pointer" onclick="db.call('patient/index', {'sort' :'birth', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="birth" :}} , 'reverse' : true {{pass}} })"> birth </td>
-                <td class="pointer" onclick="db.call('patient/index', {'sort' :'info', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="info" :}} , 'reverse' : true {{pass}} })"> info </td>
-                <td class="pointer" class="column_100" onclick="db.call('patient/index', {'sort' :'configs', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="configs" :}} , 'reverse' : true {{pass}} })"> results </td>
-{{if isAdmin:}} <td class="column_100 pointer" onclick="db.call('patient/index', {'sort' :'groups', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="groups" :}} , 'reverse' : true {{pass}} })"> groups </td> {{pass}}
-{{if isAdmin:}} <td class="column_100 pointer" onclick="db.call('patient/index', {'sort' :'creator', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="creator" :}} , 'reverse' : true {{pass}} })"> creator </td> {{pass}}
-                <td class="column_100 pointer" onclick="db.call('patient/index', {'sort' :'files', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="files" :}} , 'reverse' : true {{pass}} })"> files </td>
-                
-                
-                <td class="column5"> </td>
-                <td class="column5"> </td>
-                <td class="column5"> </td>
-            </tr>
-        </thead>
-        
-        
-       {{for row in query :}}
-           <tr class="pointer" onclick="db.call('sample_set/index', {'id' :'{{=row['sample_set_id']}}' , 'config_id' : {{=row['most_used_conf']}} } )" >
-                <td>
-                     {{ patient_name = vidjil_utils.anon_names(row['sample_set_id'], row['first_name'], row['last_name'], row['anon_allowed'])}}
-		     {{= patient_name}}
-                </td>
-                <td> {{ if row['birth'] is not None: }} {{=row['birth'] }} {{ pass }} </td>
-                <td> {{=row['info'] }} </td>
-                <td>
-                  {{ configs = [] }}
-                  {{for conf in row['conf_list'] :}}
-                    {{filename = patient_name + " (" + conf['name'] + ")"}}
-                    {{if conf['fused_file'] is not None :}}
-                      {{ configs.append(str(A(conf['name'], _href="index.html?patient=" + str(row['id']) + "&config=" + str(conf['id']), _type="text/html",
-                            _onclick="event.preventDefault();event.stopPropagation();if( event.which == 2 ) { window.open(this.href); } else { myUrl.loadURL(db, { 'patient' : '" + str(row['id']) + "' , 'config' : " + str(conf['id']) + " }, '" + filename + "' ); }"))) }}
-                    {{else:}}
-                      {{ configs.append(conf['name']) }}
-                    {{pass}}
-                  {{pass}}
-                  {{= XML(", ".join(configs)) }}
-                </td>
-{{if isAdmin:}} <td> {{=row['groups']}}</td>{{pass}}
-{{if isAdmin:}} <td> {{=row['creator']}}</td>{{pass}}
-                <td> {{=row['file_count']}} ({{=vidjil_utils.format_size(row['size'])}}) </td>
-            {{ total_file_count += row['file_count'] ; total_size += row['size'] }}
-               
-{{if isAdmin:}} <td onclick="db.call('patient/permission', {'id' :'{{=row['id']}}'} )" > <i class="icon-key" title="set permissions"></i> </td> {{else:}} <td></td> {{pass}}
-                {{if row['has_permission']:}}
-                <td onclick="db.call('patient/edit', {'id' :'{{=row['id']}}'} )" > <i class="icon-pencil-2" title="edit patient information"></i> </td>
-                <td onclick="db.call('patient/confirm', {'id' :'{{=row['id']}}'} )" > <i class="icon-erase" title="delete patient"></i> </td>
-                {{else:}}  <td></td><td></td>{{pass}}
-            </tr>
-        {{pass}}
-
-    </table>
-    <table class="db_table" id="db_fixed_header"></table>
-</div>
-
-<div class="db_block">
-    <div class="db_block_left">
-
-{{if auth.can_create_patient():}}
-<span class="button2" onclick="db.call('patient/add')"> + new patients </span>
-<span class="button2" onclick="db.call('sample_set/custom', {'filter': '{{=request.vars['filter']}}' })"> compare samples/patients </span>
-{{else:}}
-<!-- <span class="button2 inactive" onclick="db.call('patient/add')" title="you don't have permission to create new patient"> add patient </span> -->
-{{pass}}
-
-  </div>
-  <div class="db_block_right">
-  <br />
-  {{ =len(query) }} patients, {{ =total_file_count }} files ({{ =vidjil_utils.format_size(total_size) }})
-  </div>
-</div>

server/web2py/applications/vidjil/views/run/confirm.html

-{{extend 'db_layout.html'}}
-{{import vidjil_utils}}
-
-{{('message' in globals())}}
-{{if 'message' in globals():}}
-
-{{
-data_count = 0 
-run_name = db.run[request.vars["id"]].name
-}}
-<div>
-    <h3>{{=message}}: {{=run_name}}
-    </h3>
-    
-    Are you sure you want to delete the run {{=run_name}} ?</br>
-    This action cannot be undone.
-
-    <div class="center"> 
-        <button onclick="db.call('run/delete', {'id' :'{{=request.vars["id"]}}'} )">delete</button>
-        <button onclick="db.call('run/index')">cancel</button>
-    </div>
-</div>
-    
-{{elif 'content' in globals():}}
-{{=content}}
-{{else:}}
-{{=BEAUTIFY(response._vars)}}
-{{pass}}

server/web2py/applications/vidjil/views/run/index.html

-{{extend 'db_layout.html'}}
-{{import vidjil_utils}}
-
-{{total_file_count = 0 ; total_size = 0}}
-
-<h3></h3>
-
-<div class="db_block">
-    <div class="db_block_left">
-        search
-        <input id="db_filter_input" type="text" value="{{=request.vars["filter"]}}"  onchange="db.call('patient/index', {'filter' : this.value} )">
-    </div>
-</div>
-
-<div id="db_table_container">
-    <table class="db_table" id="table">
-
-
-        <thead>
-            <tr><td class="column_200 pointer" onclick="db.call('run/index', {'sort' :'name', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="name" :}} , 'reverse' : true {{pass}} })"> name </td>
-                
-                <td class="column_100 pointer" onclick="db.call('run/index', {'sort' :'run_date', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="run_date" :}} , 'reverse' : true {{pass}} })"> date </td>
-                
-                <td class="pointer" onclick="db.call('run/index', {'sort' :'info', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="info" :}} , 'reverse' : true {{pass}} })"> info </td>
-                
-                <td class="pointer" class="column_100" onclick="db.call('run/index', {'sort' :'configs', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="configs" :}} , 'reverse' : true {{pass}} })"> configs </td>
-                
-{{if isAdmin:}} <td class="column_100 pointer" onclick="db.call('run/index', {'sort' :'groups', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="groups" :}} , 'reverse' : true {{pass}} })"> groups </td> {{pass}}
-                
-{{if isAdmin:}} <td class="column_100 pointer" onclick="db.call('run/index', {'sort' :'creator', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="creator" :}} , 'reverse' : true {{pass}} })"> creator </td> {{pass}}
-                
-                <td class="column_100 pointer" onclick="db.call('run/index', {'sort' :'files', 'filter' : '{{=request.vars["filter"]}}'
-                  {{if not reverse and request.vars["sort"]=="files" :}} , 'reverse' : true {{pass}} })"> files </td>
-                
-                
-                <td class="column5"> </td>
-                <td class="column5"> </td>
-                <td class="column5"> </td>
-            </tr>
-        </thead>
-        
-        
-       {{for row in query :}}
-           <tr class="pointer" onclick="db.call('sample_set/index', {'id' :'{{=row['sample_set_id']}}' , 'config_id' : {{=row['most_used_conf']}} } )" >
-                <td> {{=row['name']}} </td>
-                <td> {{ if row['run_date'] is not None: }} {{=row['run_date'] }} {{ pass }} </td>
-                <td> {{=row['info']}} </td>
-                <td>
-                  {{ configs = [] }}
-                  {{for conf in row['conf_list'] :}}
-                    {{filename = row['name'] + " (" + conf['name'] + ")"}}
-                    {{if conf['fused_file'] is not None :}}
-                      {{ configs.append(str(A(conf['name'], _href="index.html?sample_set=" + str(row['sample_set_id']) + "&config=" + str(conf['id']), _type="text/html",
-                            _onclick="event.preventDefault();event.stopPropagation();if( event.which == 2 ) { window.open(this.href); } else { myUrl.loadUrl(db, { 'sample_set_id' : '" + str(row['sample_set_id']) + "' , 'config' : " + str(conf['id']) + " }, '" + filename + "' ); }"))) }}
-                    {{else:}}
-                      {{ configs.append(conf['name']) }}
-                    {{pass}}
-                  {{pass}}
-                  {{= XML(", ".join(configs)) }}
-                </td>
-{{if isAdmin:}} <td> {{=row['groups']}}</td>{{pass}}
-{{if isAdmin:}} <td> {{=row['creator']}}</td>{{pass}}
-                <td> {{=row['file_count']}} ({{=vidjil_utils.format_size(row['size'])}}) </td>
-            {{ total_file_count += row['file_count'] ; total_size += row['size'] }}
-               
-{{if isAdmin:}} <td onclick="db.call('run/permission', {'id' :'{{=row['id']}}'} )" > <i class="icon-key" title="set permissions"></i>  </td> {{else:}} <td></td> {{pass}}
-                {{if row['has_admin_permission']:}}
-                <td onclick="db.call('run/edit', {'id' :'{{=row['id']}}'} )" >  <i class="icon-pencil-2" title="edit run information"></i> </td>
-                <td onclick="db.call('run/confirm', {'id' :'{{=row['id']}}'} )" >  <i class="icon-erase" title="delete run"></i> </td>
-                {{else:}}  <td></td><td></td>{{pass}}
-            </tr>
-        {{pass}}
-
-    </table>
-    <table class="db_table" id="db_fixed_header"></table>
-</div>
-
-<div class="db_block">
-    <div class="db_block_left">
-
-{{if auth.can_create_patient():}}
-<span class="button2" onclick="db.call('run/add')"> + new runs </span>
-<span class="button2" onclick="db.call('sample_set/custom', {'filter': '{{=request.vars['filter']}}' })"> compare samples/runs </span>
-{{else:}}
-<!-- <span class="button2 inactive" onclick="db.call('patient/add')" title="you don't have permission to create new patient"> add patient </span> -->
-{{pass}}
-
-  </div>
-  <div class="db_block_right">
-  <br />
-  {{ =len(query) }} runs, {{ =total_file_count }} files ({{ =vidjil_utils.format_size(total_size) }})
-  </div>
-</div>